Mitochondria are responsible for the majority of energy production in our cells. A small by vital number of the proteins that carry out this function are encoded in mitochondrial DMA (mtDNA). Mitochondria carry out a series of metabolic reactions to support the replication of their mtDNA, with all of the enzymes of this metabolism encoded in the nuclear DMA. Mutations in these nuclear genes cause a family of diseases that result in the depletion or enhanced mutation of mtDNA and the subsequent loss of the cell function or cell death. We propose to develop a computational model of this critical metabolism and to apply this model to five genetic diseases to understand the pathology of these diseases. The development and testing of this computational model will be done in parallel with experiments in the laboratory of the co-Pi. Specific Aim 1: Develop and test a simulation of mitochondrial deoxynucleotide metabolism. This metabolic network consists of four parallel tracks linked by many competitive and other inhibitions. The complexities of this metabolic network require a simulation to follow the dynamics of the metabolism. Specific Aim 2: Use the simulations to determine the flow of deoxynucleotides through this metabolic network. Deoxynucleotides can enter or leave the mitochondrion at two points in the metabolic network, allowing complicated flows of material through this system. Specific Aim 3: Develop a simulation of the fidelity of polymerase-gamma. Errors in the mitochondrial DMA polymerase activity are the mechanism of pathogenesis in these diseases. Specific Aim 4: Apply the simulation to five genetic diseases. The diseases are mitochondrial DMA depletion syndrome, autosomal dominant and recessive progressive external opthalmoplegia (adPEO and arPEO), mitochondrial neurogastrointestinal encephalomyapathy (MNGIE), and Amish microcephaly (MCPHA). Specific Aim 5: Apply this model to ischemia and cancer. In these common medical conditions nucleotide metabolism is altered and mtDNA mutations or depletion occur, possibly playing a role in the pathogenesis of these conditions. Public Health Relevance: This research concerns a set of genetic diseases which are often fatal in early childhood. It also concerns ischemia and cancer, two important health problems in the general population.